I made a similiar recipe using the pilsner malt for the 90min. Then I just made a 60min using english 2 row. I am curious what the difference would be. I used warrior simcoe and amarillo hops for both.

Divide the hop amounts into 10 additions, added every 6 minutes in Beersmith. It took me a LONG time to add 30 hop additions into beersmith, but the IBUs came back way low. Considering the inaccuracy of the BYO recipe, i'm going with my gut, that little hops won't equal 90 IBUs

90 minute is 8-9 SRM if i had to guess, no more. So I'm cutting back the amber to 5% or so.
Hops are as follows:
Amarillo: 3oz
Simcoe: 1oz
Warrior: 1oz
Divide evenly into 10 doses, and add every 6min.
Dry hop per the recipe above, and ferment with two packs of s-04

I am interested in how your new recipe turns out as I brew the 90 Min BYO clone quite a bit. I really like it, but it is off from the original a little and I would like to get as close as I can. I noticed in that interview that he also says "pile on the hops in the end of the boil and in the fermenter" instead of equal additions throughout the boil. Any thoughts on changing this as well?

BTW, I have 2oz Amarillo @ 8%, .5oz Warrior @ 15%, and .6 of Simcoe @ 13% and my IBU's say 89 in Beersmith. Maybe that is how BYO came up with 90IBU's by putting them in the software that way for the entire 90min. Just a thought.